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Literature summary for 3.5.1.88 extracted from

  • Cui, K.; Lu, W.; Zhu, L.; Shen, X.; Huang, J.
    Caffeic acid phenethyl ester (CAPE), an active component of propolis, inhibits Helicobacter pylori peptide deformylase activity (2013), Biochem. Biophys. Res. Commun., 435, 289-294.
    View publication on PubMed
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Crystallization (Commentary)

Crystallization (Comment) Organism
ligand-free enzyme, and complxed with inhibitors actinonin and caffeic acid phenethyl ester, hanging drop vapour diffusion method, condition screening, using 0.1 M HEPES, pH 7.5, 70% v/v MPD, mixing of 0.001 ml protein and reservoir solution each, and equilibration against 0.5 ml of reservoir solution, 17°C, X-ray diffraction structure determination and analysis at 1.66-1.70 A resolution Helicobacter pylori

Inhibitors

Inhibitors Comment Organism Structure
(2R)-N-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-2-[[formyl(hydroxy)amino]methyl]hexanamide i.e. BB-3497 Helicobacter pylori
(2R)-N-[(2S)-1-{4-[(2H-1,3-benzodioxol-5-yl)methyl]piperazin-1-yl}-3,3-dimethyl-1-oxobutan-2-yl]-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanamide i.e. BB-83698 Helicobacter pylori
actinonin 95% inhibition at 0.01 mM, competitive, locates near the active site and plugs the substrate tunnel to prevent the substrate from accessing the catalytic site Helicobacter pylori
caffeic acid phenethyl ester CAPE, an active component of propolis, 75% inhibition at 0.01 mM, the competitive inhibitor blocks the substrate entrance, preventing substrate from approaching the active site, but CAPE does not have chelate interaction with HpPDF and does not disrupt the metal-dependent catalysis Helicobacter pylori
additional information inhibition mechanism and kinetics, overview. No significant inhibition by caffeic acid, ferulic acid, chlorogenic acid, genistein, curcumin, naringenin, hesperitin, chrysin,apigenin, luteolin, kaempferol, myricetin, silibinin, and rutin at 0.01 mM Helicobacter pylori
N-formylhydroxylamine i.e. LBM-415 Helicobacter pylori
N-[(2R)-2-(cyclopentylmethyl)-3-(2-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}hydrazinyl)-3-oxopropyl]-N-hydroxyformamide i.e. GSK1322322 Helicobacter pylori
tert-butyl 1-[(2R)-2-[2-(hydroxyamino)-2-oxoethyl]hexanoyl]-L-prolinate i.e. VRC-3375 Helicobacter pylori
VRC-4307
-
 Helicobacter pylori

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ dependent on, metalloenzyme Helicobacter pylori

Organism

Organism UniProt Comment Textmining
Helicobacter pylori
-
-
-

Synonyms

Synonyms Comment Organism
PDF
-
 Helicobacter pylori

IC50 Value

IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
0.00017
-
 pH and temperature not specified in the publication Helicobacter pylori actinonin
0.00402
-
 pH and temperature not specified in the publication Helicobacter pylori caffeic acid phenethyl ester